Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean

Abstract A high-throughput genotyping platform with customized flexibility, high genotyping accuracy and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay panels were selected from the SoySNP50K, 40K, 20K and 10K, containing 41541, 20748 and 9670 SNP markers, respectively, for genotyping-by-target sequencing (GBTS). Fifteen representative accessions were used to assess the accuracy and consistency of the SNP alleles determined by the SNP panels and sequencing platform. SNP alleles were 99.87% identical between technical replications and 98.86% identical between the 40K SNP GBTS panel and 10× resequencing analysis. The GBTS method was also accurate because the genotypic dataset of the 15 representative accessions correctly revealed the pedigree of the accessions and the biparental progeny datasets correctly constructed the linkage maps of the SNPs. The 10K panel was also used to genotype two parent-derived populations and analyze QTLs controlling 100-seed weight, resulting in the identification of the stable associated genetic locus Locus_OSW_06 on chromosome 06. The markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, 40K, 20K and 10K costs were reduced by 5.38% and 139.78%, 27.27% and 189.61%, and 55.56% and 253.97%, respectively. Low-cost genotyping panels could facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and soybean genomic selection.